DNA probe based colorimetric method for detection of rifampicin resistance of Mycobacterium tuberculosis.

Rifampicin resistance of Mycobacterium tuberculosis is due to the occurrence of point mutations of the rpoB gene and the site of mutations vary geographically. Commercialized molecular based methods are not able to comprehensively detect rifampicin resistance as they target a limited number of gene mutations which are thought to be common. The aim of the study was to establish a low cost DNA probe based colorimetric method that can be customized for detection of rifampicin resistance of M. tuberculosis. Thus, enzyme-linked oligosorbent assay (ELOSA) was developed for the detection of polymerase chain reaction (PCR) amplified fragments of rpoB gene of M. tuberculosis DNA on microtiter plates. Forty two M. tuberculosis isolates (rifampicin resistant and susceptible isolates identified by agar proportion method) were used for developing and validating the assay. The point mutations of resistant isolates had been previously determined by DNA sequencing. Two fragments of rpoB gene were labeled with digoxigenin by PCR. The amplified products were hybridized with selected allele specific probes for three mutations and its wild types (six probes) which were captured onto streptavidin coated microtiter plates and detected by color development. Both sensitivity and specificity of all probes were ≥96% and there was excellent discrimination (area under the curve (AUC)>0.9) between rifampicin susceptible cases and resistant cases. The probe-based colorimetric assay (PCR-ELOSA) developed in this study showed good agreement with reference mutations that were confirmed by DNA sequencing. In conclusion, PCR-ELOSA is a reliable and economical assay that can be customized for detection of rifampicin resistance.

The manual mycobacteria growth indicator tube and the nitrate reductase assay for the rapid detection of rifampicin resistance of M. Tuberculosis in low resource settings.

BACKGROUND: Tuberculosis (TB) is a disease of poverty that contributes significantly to ill-health in developing countries. Drug resistant TB is a major challenge to disease control. Early diagnosis and rapid determination of drug sensitivity is of paramount importance in eradication of TB. Although automated liquid culture based methods are available for rapid detection of drug resistance, the high cost of these tests prevent them from being used routinely in low resource settings. This study compares two phenotypic methods, the manual Mycobacteria Growth Indicator Tube (MGIT) and the Nitrate Reductase Assay (NRA) in liquid medium, with the agar proportion method (APM), the gold standard for susceptibility testing of Mycobacterium tuberculosis. METHODOLOGY: Fourteen day old M. tuberculosis strains (n=373) grown on solid media were used for drug susceptibility testing by APM, NRA and the manual MGIT method. Rifampicin free and rifampicin incorporated (final concentration, 1 µg/ml) media were inoculated with the recommended concentrations of mycobacterial suspensions and incubated at 37°C in 5% CO2. In the APM, the proportion of colonies in the drug containing medium was determined. In the NRA, the colour change in the medium was compared with a standard colour series after day 6 and day 12 of incubation. Growth in the MGIT was detected using the manual MGIT reader from day 2 onwards. The 2 methods were compared with the gold standard, APM to determine sensitivity and specificity and agreement between the methods was calculated using kappa statistics. RESULTS: Thirty one (31) rifampicin resistant isolates were identified. When compared with the APM, the sensitivity of detection of rifampicin resistance was 85% for the NRA and 93% for the manual MGIT and the specificity was 99% and 100% respectively. Both assays, NRA (κ=0.86) and manual MGIT method (κ= 0.94) were in excellent agreement with the APM. The mean turnaround time for manual MGIT method and NRA were 08 days and 10 days respectively. CONCLUSION: The NRA in liquid medium and manual MGIT are useful alternatives to APM for drug susceptibility testing of M. tuberculosis in low resource settings.